Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / thelovelab/tximeta issues and pull requests

#82 - Tximeta does not recognize prebuild TxDb objects for custom transcriptomes

Issue - State: closed - Opened by alexdhill 4 months ago - 2 comments

#81 - Support for `oarfish` quants

Issue - State: closed - Opened by mikelove 8 months ago - 4 comments

#80 - issue importing alevin files with tximeta 1.20.0

Issue - State: closed - Opened by csoneson about 1 year ago - 3 comments

#79 - a problem after installing tximeta

Issue - State: closed - Opened by WesleyChan0917 about 1 year ago - 4 comments

#78 - Add genome2UCSC mapping for GRCm39

Pull Request - State: closed - Opened by csoneson about 1 year ago - 3 comments

#77 - Change genome build to GRCm39 for GENCODE release M26 and later

Pull Request - State: closed - Opened by csoneson about 1 year ago - 2 comments

#76 - Issue with cache

Issue - State: closed - Opened by guidohooiveld over 1 year ago - 2 comments

#75 - When disconnected still sometimes error trying to get seqinfo

Issue - State: open - Opened by mikelove over 1 year ago
Labels: bug

#74 - Convert list from tximport() to SummarizedExperiment object

Issue - State: closed - Opened by ElvaWong over 1 year ago - 2 comments

#73 - summarizeToGene should use most abundant isoform for GRanges

Issue - State: closed - Opened by mikelove over 1 year ago - 1 comment
Labels: enhancement

#71 - SummarizedExperiment or DESeqDataSet Leves Null

Issue - State: closed - Opened by lulumagic7 almost 2 years ago - 2 comments

#69 - GENCODE transcriptome v42 not recognised

Issue - State: closed - Opened by GiBacci about 2 years ago - 1 comment

#68 - Tximeta for novel transcripts by stringite

Issue - State: closed - Opened by karlaarz about 2 years ago - 12 comments

#67 - Unsuccessful connection to AnnotationHub blocks tximeta on HPC

Issue - State: closed - Opened by danilotat over 2 years ago - 5 comments

#66 - Error in checkAssays2Txps

Issue - State: closed - Opened by karlaarz over 2 years ago - 5 comments

#65 - GENCODE - Mus musculus - release M28 not loading ok

Issue - State: closed - Opened by AMChalkie over 2 years ago - 13 comments

#64 - Getting "couldn't find matching transcriptome" with Gencode 40

Issue - State: closed - Opened by jwtobias over 2 years ago - 3 comments

#62 - tximeta returns Error: lexical error: invalid string in json text.

Issue - State: closed - Opened by Shellfishgene almost 3 years ago - 2 comments

#61 - If skipMeta=TRUE, still could put Salmon version etc

Issue - State: open - Opened by mikelove almost 3 years ago

#59 - DGElist coldata

Pull Request - State: closed - Opened by csoneson about 3 years ago - 2 comments

#58 - tximeta UCSC not co-operating in terms of mm10

Issue - State: closed - Opened by justinjacobse over 3 years ago - 2 comments

#56 - cached transcript fails to build

Issue - State: closed - Opened by JudithR over 3 years ago - 9 comments

#55 - addExons throws error: in bfcrpath(bfc, txdbName) : not all 'rnames' found or unique.

Issue - State: closed - Opened by matmu almost 4 years ago - 2 comments

#54 - none of the transcripts in the quantification files are in the GTF

Issue - State: closed - Opened by ibekere almost 4 years ago - 9 comments

#53 - dtuScaledTPM doesn't work

Issue - State: open - Opened by mikelove almost 4 years ago

#52 - Should tximeta find any available TxDb/EnsDb when hash is identical?

Issue - State: open - Opened by mikelove almost 4 years ago
Labels: enhancement

#51 - did not find matching TxDb via 'AnnotationHub'

Issue - State: closed - Opened by AbbyFeng almost 4 years ago - 2 comments

#49 - Make sure loading works even if bfcLoc is NULL.

Pull Request - State: closed - Opened by csoneson about 4 years ago - 3 comments

#48 - Error with 'download.file' on Linux cluster

Issue - State: closed - Opened by lmweber about 4 years ago - 2 comments

#47 - Bioconda version still 1.6.2

Issue - State: closed - Opened by matmu about 4 years ago - 3 comments

#45 - batch processing compatibility

Issue - State: closed - Opened by stolarczyk about 4 years ago - 3 comments

#44 - Extrating/adding gene_name to transcript level data

Issue - State: closed - Opened by kvittingseerup about 4 years ago - 5 comments

#43 - Is it possible to extract transcript nucleotide sequence?

Issue - State: closed - Opened by kvittingseerup about 4 years ago - 5 comments

#42 - Request: addCDS() function

Issue - State: closed - Opened by kvittingseerup about 4 years ago - 6 comments

#41 - Tximeta, Salmon, and imported TPM

Issue - State: closed - Opened by FrAoJm over 4 years ago - 5 comments

#40 - Check if GENCODE TxDb exists in AnnotationHub

Issue - State: closed - Opened by mikelove over 4 years ago - 3 comments

#39 - Add support for new RefSeq seqlevelsStyle functionality

Issue - State: open - Opened by mikelove over 4 years ago

#36 - Error in splitSE

Issue - State: closed - Opened by cnk113 over 4 years ago - 1 comment

#33 - Issue with finding matching exome/makeLinkedTxome

Issue - State: closed - Opened by malawsky over 4 years ago - 4 comments

#32 - Customized import of alevin bootstrap counts

Issue - State: closed - Opened by k3yavi over 4 years ago - 1 comment
Labels: enhancement

#31 - Allow setting cache directory via environment variable

Issue - State: closed - Opened by csoneson over 4 years ago - 2 comments
Labels: enhancement

#30 - Add splitSE function

Pull Request - State: closed - Opened by csoneson over 4 years ago

#29 - Modified Ensembl GTF parsing error

Issue - State: closed - Opened by jma1991 over 4 years ago - 7 comments

#28 - biocache file problem

Issue - State: closed - Opened by klai001 almost 5 years ago - 2 comments

#27 - Add txp IDs as CharacterList when summarizing to gene level

Issue - State: closed - Opened by mikelove almost 5 years ago - 1 comment
Labels: enhancement

#26 - Add info about duplicates to output SE

Issue - State: closed - Opened by csoneson almost 5 years ago - 14 comments

#25 - Error: Could not connect to database:

Issue - State: closed - Opened by Knievl almost 5 years ago - 2 comments

#24 - GENCODE transcriptome hashes not recognized

Issue - State: closed - Opened by drdariarago almost 5 years ago - 20 comments

#23 - Generate Methods section boilerplate text

Issue - State: open - Opened by mikelove almost 5 years ago - 5 comments
Labels: enhancement

#22 - Adapt makeLinkedTxome to Salmon 1.0.0 index

Pull Request - State: closed - Opened by csoneson about 5 years ago - 1 comment

#21 - lexical error returned when running makeLinkedTxome

Issue - State: closed - Opened by wzmin about 5 years ago - 14 comments

#20 - multiple sample input with type = "alevin"

Issue - State: closed - Opened by csoneson about 5 years ago - 3 comments

#19 - Error when making linked txome

Issue - State: closed - Opened by Norbittner about 5 years ago - 8 comments

#18 - Also stash ranges in BiocFileCache

Issue - State: closed - Opened by mikelove over 5 years ago

#17 - error in addIds

Issue - State: closed - Opened by AnnaSawicka over 5 years ago - 3 comments

#16 - Paired txomes (human + mouse Gencode)

Issue - State: closed - Opened by mikelove about 6 years ago - 3 comments

#15 - ID conversion and tximport arguments

Issue - State: closed - Opened by koenvandenberge about 6 years ago - 12 comments

#14 - Extracting exon-level information

Issue - State: closed - Opened by kvittingseerup about 6 years ago - 2 comments

#13 - Missing my favorite organism/source [please add as a comment to this issue]

Issue - State: open - Opened by mikelove about 6 years ago - 8 comments
Labels: enhancement

#12 - Make DGEList example for vignette

Issue - State: closed - Opened by mikelove about 6 years ago

#11 - Keep gene ID for non-Ensembl transcriptomes

Pull Request - State: closed - Opened by csoneson about 6 years ago - 1 comment

#10 - Keeping transcript and gene information in the same object - gencode

Issue - State: closed - Opened by sorjuela over 6 years ago - 2 comments

#9 - Stand-alone program to upload quant dirs to GEO (from Kaspar Hansen)

Issue - State: open - Opened by mikelove over 6 years ago
Labels: enhancement

#8 - Add argument for manually providing hash (from Nathan Sheffield)

Issue - State: closed - Opened by mikelove over 6 years ago - 1 comment

#7 - Renaming duplicate transcripts for Ensembl

Issue - State: closed - Opened by mikelove over 6 years ago - 3 comments

#6 - What if one can't connect to internet

Issue - State: closed - Opened by mikelove over 6 years ago - 1 comment

#5 - Small differences in derived txomes relative to reference txome (possible?)

Issue - State: open - Opened by ttriche over 6 years ago - 1 comment
Labels: enhancement

#4 - How to ask user only once for best BiocFileCache location

Issue - State: closed - Opened by mikelove almost 7 years ago

#3 - Proper sequence length and genome for GRC

Issue - State: closed - Opened by mikelove about 7 years ago - 1 comment

#2 - Linked transcriptomes (formerly "derived")

Issue - State: closed - Opened by mikelove about 7 years ago - 2 comments

#1 - Initial thoughts

Issue - State: closed - Opened by PeteHaitch about 7 years ago - 5 comments